<!DOCTYPE html> 

<html>

<head>

<style>
</style>

<title>Human GRCh38 :: Dalliance</title> 
<script language="javascript" src="../build/dalliance-all.js"></script>

<script language="javascript">
var b = new Browser({
   chr:                 '22',
    viewStart:           30300000,
    viewEnd:             30500000,
    cookieKey:           'human-grc_h38',

    coordSystem: {
      speciesName: 'Human',
      taxon: 9606,
      auth: 'GRCh',
      version: '38',
      ucscName: 'hg38'
    },

    chains: {

      hg19ToHg38: new Chainset('http://www.derkholm.net:8080/das/hg19ToHg38/', 'GRCh37', 'GRCh38',
                               {
                                  speciesName: 'Human',
                                  taxon: 9606,
                                  auth: 'GRCh',
                                  version: 37,
                                  ucscName: 'hg19'
                               })
    },

    sources:          [{name:                 'Genome',
                       twoBitURI:            'http://www.biodalliance.org/datasets/hg38.2bit',
                       tier_type: 'sequence'}


                      ,{name: 'GENCODE',
                       desc: 'Gene structures from GENCODE 20',
                       bwgURI: 'http://www.biodalliance.org/datasets/GRCh38/gencode.v20.annotation.bb',
                       stylesheet_uri: 'http://www.biodalliance.org/stylesheets/gencode2.xml',
                       collapseSuperGroups: true,
                       trixURI: 'http://www.biodalliance.org/datasets/GRCh38/gencode.v20.annotation.ix'}

                      ,{name: 'GENCODEv19',
                       desc: 'Gene structures from GENCODE 19',
                       bwgURI: 'http://www.biodalliance.org/datasets/gencode.bb',
                       stylesheet_uri: 'http://www.biodalliance.org/stylesheets/gencode.xml',
                       collapseSuperGroups: true,
                       pennant: 'http://genome.ucsc.edu/images/19.jpg',
                       trixURI: 'http://www.biodalliance.org/datasets/gene-index.ix',
                       mapping: 'hg19ToHg38'}

                      ,{name: 'Repeats',
                        desc: 'Repeat annotation from UCSC', 
                        bwgURI: 'http://www.biodalliance.org/datasets/GRCh38/repeats.bb',
                        stylesheet_uri: 'http://www.biodalliance.org/stylesheets/bb-repeats2.xml'}

                      ,{name: 'SNPs',
                        tier_type: 'ensembl',
                        species:'human',
                        type: 'variation',
                        disabled: true,
                        featureInfoPlugin: function(f, info) {
                          if (f.id) {
                            info.add('SNP', makeElement('a', f.id, {href: 'http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=' + f.id, target: '_newtab'}));
                          }
                        }
                       }

    ],

    prefix: '../',
    fullScreen: true,

    browserLinks: {
      Ensembl: 'http://www.ensembl.org/Homo_sapiens/Location/View?r=${chr}:${start}-${end}',
      UCSC: 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr${chr}:${start}-${end}',
      Sequence: 'http://www.derkholm.net:8080/das/hg19comp/sequence?segment=${chr}:${start},${end}'
    },

    hubs: ['http://ngs.sanger.ac.uk/production/ensembl/regulation/hub.txt', {url: 'http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt', genome: 'hg19', mapping: 'hg19ToHg38'}],
  });

</script>
</head>

<body>
<div id='svgHolder'>Failed to load the Biodalliance genome browser.  Have you run "gulp"?</div>
</body>
</html>

